Substrate oxidation was compared during different high-intensity intermittent exercise (HIIE) protocols in patients with heart failure and reduced ejection fraction (HFREF). Eighteen males with HFREF (58.8 ± 9 years) were randomly assigned to 4 different HIIEs: 30 seconds (A and B) or 90 seconds (C and D) at 100% peak power output, with passive (A and C) or active recovery (50% of peak power output; B and D). Each HIIE protocol was separated by 1 week. Substrate oxidation (carbohydrate [CHO] and lipid: in g/min and in %) was calculated with gas exchange analysis. A 2-way analysis of variance and Bonferroni post hoc test were used (P ≤ 0.05) to compare CHO and lipid oxidation during the 4 HIIEs. Protocols with passive recovery (A and C) resulted in significantly lower quantitative CHO oxidation (g/min) (interaction, P < 0.001) compared to modes with active recovery (B and D). Quantitative lipid oxidation (g/min) was significantly lower in protocol C compared to the 3 other HIIE protocols (interaction, P < 0.001). In patients with HFREF, shorter HIIE bouts with passive recovery oxidize less CHO and more lipids (quantitatively) compared to the other HIIE protocols. This might be taken into account the exercise training prescription and might influence muscle metabolism adaptations.